Before the Storm
by RascalFlattsS
Summary: Orion is the best computer programmer the CIA ever had. And the Ring wants him. How do they find him? By kidnapping everyone's favorite CIA agent with an Intersect in his head of course. Can team Bartowski save Chuck and his dad and stop the Ring's plan?
1. Chapter 1

Before the Storm

By RascalFlattsS

Disclaimer: Do not own Chuck.

Summary: Orion is the best computer programmer the CIA ever had. And the Ring wants him. How do they find him? By kidnapping everyone's favorite CIA agent with an Intersect in his head of course. Can team Bartowski save Chuck and his dad and stop the Ring's evil plans in time?

Plenty of Chuck whumpage.

Some mild swearing. Nothing too bad. And maybe a few little spoilers but nothing too big, I promise.

Note: Takes place in the beginning of Season 3. I know that Ellie and Devon moved out within the first or second episode but for the story, I wanted to explore Chuck's and Ellie's relationship and for the purpose of the story, it flows better if Chuck still lives with Ellie and Devon.

Any spellings and grammar errors are mine. The computer just needs to get smarter than I am

* * *

><p><em>Secret Evil Guy Hiding Place-Location Unknown<em>

"Any luck?" asked the man taking another puff from his cigar.

"None yet, sir," replied the technician.

"He couldn't have just fallen off the face of the earth!" shouted the man.

"We'll keep searching, sir," said the technician.

The man sighed and stormed off. He slammed the door to his office, ignoring the other man already in there. "Damn it Carl! At this rate, we'll never find him!"

"Patience James," replied Carl. "Orion didn't just fall off the face of the earth."

"Apparently he has," said James. "We can't seem to find him."

"Oh course you're not going to find him," said Carl smiling, "Orion is the type of man where if he doesn't want to be found, you're not going to find him."

"Then what do you suggest we do?" asked James.

"It's simple," said Carl. "I'm surprised to you didn't think of it sooner." Carl paused. "We let Orion come to us."

"And how exactly do you suggest we do that?" asked James.

Carl rolled his eyes and pulled a vanilla folder. He tossed it on the desk. James picked it up. A picture was paper clipped to the top.

"It's just a matter of using the right bait," said Carl.

"Orion has a family?" asked James.

Carl nodded, "His daughter Ellie and her husband Devon." He pointed to Ellie and Devon in the picture. "Both are doctors. And both potential targets. But his son-"he pointed to Chuck-"this is the potential goldmine."

"Why the son?" asked James.

"Read the file," said Carl. "Young Chuck has followed in his father's footprints." He smiled, "You get the son and daddy dearest will come running."

* * *

><p><em>Barktowski-Woodcomb Residence-Burbank, California<em>

"CHUCK!"

Chuck Bartowski groaned and rubbed his eyes. He rolled over and looked at his alarm clock. 7:30 am. And he had gotten home at 4 am.

Being a spy was definitely cutting into his sleep.

"CHUCK!"

Chuck groaned and rolled up and out of bed. He walked out into the kitchen. "Good morning," he mumbled. He looked at his sister, "Why are you yelling so loud?"

"Because of this," said Ellie. She grabbed his hand and dragged him into the living room. "You left your stuff out in the middle of the room again Chuck! I almost broke my neck tripping over it."

"Sorry Ellie," said Chuck. He picked up his backpack. "Won't happen again."

"I also noticed you didn't get home till 4 am," said Ellie. "Where were you?"

"I was at the Buy More," said Chuck. "Big Mike had me doing inventory."

"Till 4 am?" asked Ellie.

"No," said Chuck. "I was only supposed to stay an hour or so and do inventory but…" Chuck signed rubbing the back of his neck, "I took a quick break in the home theatre room and I guess I must have fallen asleep because the next thing I knew it was 3:30 in the morning."

Ellie sighed. "You're working too much Chuck," she said. "You need to get a different job-a better job. You have a Stanford decree for crying out loud!"

"Ellie, sweetie," said Devon. He came up behind Ellie and wrapped his arms around her, "Give Chuck a break. He doesn't need a lecture right away in the morning."

"Thank you Awesome," said Chuck.

"I just don't want to see you waste your life," said Ellie.

"I'm not wasting my life," said Chuck.

"Working at the Buy More?" asked Ellie. "What do you call that? Chuck, you could do so much more if you only applied yourself."

"Ellie," started Chuck.

"Whatever Chuck," said Ellie. "Waste your life. See if I care." She grabbed her purse and marched out the door, slamming it shut behind her.

"Great," said Chuck. "That's just what I needed."

"Don't worry bro," said Devon. "I'll talk to her."

"Thanks Devon," said Chuck. He rubbed his eyes and reached for the coffee pot.

"Another late night mission?" asked Devon.

Chuck nodded, "Yeah. Luckily I have the day off from Buy More, so I should be able to catch some sleep."

"Good," said Devon. "You work too hard Chuck."

Chuck smiled, "Tell me about it."

"I have to go to work," said Devon. He paused, "You know Ellie is only looking out for your best interest, right?"

Chuck nodded, "I know."

* * *

><p>Chuck tried to go back to sleep but no matter how he tried, he couldn't go back to sleep. He kept going over the fight with Ellie. Finally after a half hour, Chuck finally gave up on the idea of trying to sleep.<p>

It was quarter to eight. He wasn't due at Castle till one. That gave him plenty of time to go to the hospital and straighten things out with Ellie.

Satisfied with his plan, he got up and took a quick shower. He dressed in a pair of jeans, a long sleeve white shirt with a red t-shirt on top and his favorite tennis shoes.

Chuck was sitting at the breakfast table eating a bowl of cereal when he heard a noise from coming down from the hall. Chuck looked up startled.

He waited a few moments when he thought he heard the sound of footsteps. He got up and started to walk down the hall. He held his cell phone in his hand, with his finger on the speed dial to call Sarah for back-up.

He searched the bathroom and his room and found nothing. He walked into Ellie's and Devon's room. He barely made it into the room when a large force slammed into him. Chuck fell backwards, slamming his head against the floor. His cell phone went flying out of his hand.

Chuck felt two rough hands grab him and pull him up. Chuck struggled but the two men (who were the same build of John Casey) had him in a tight grip.

A man stepped out of the shadows. He had thick blonde hair that was combed back. He had a large scar on his check.

Chuck felt himself flash. He saw the entire file of the man before him: Carl Rottweiler, rogue spy believed to be working for the Ring. Carl worked on the team that built the Intersect.

The flash ended and Chuck shook his head, trying to clear his head.

"I see that you had flashed," said Carl. "And yes Chuck, I know all about the Intersect and I know that you already know who I am."

"What do you want?" asked Chuck.

"Isn't it obvious?" asked Carl.

"You're here for the Intersect," said Chuck.

"No, not really," said Carl. "I don't really give a rat's ass about the Intersect. I helped build it; if I wanted another, I would just build it."

"Then what the hell do you want?" asked Chuck.

"You," said Carl, smiling. "You and I are going to take a field trip. We can do the easy way or the hard way."

Chuck smiled as he flashed on his karate skills, "I prefer the hard way." He kicked the guy on the right in the knee. Once he let go, Chuck used his free hand to punch the guy on his left straight in the face. The guy stumbled back and hit a picture frame, knocking it to the floor. Once he was taken care of, Chuck turned his attention to the other man, fighting with him.

The bad guy kicked Chuck in the shoulder, causing him to stumble. He knocked into a table over all the items on top. Chuck regained his balance and charged forward. The bad guy pulled out a knife and tried to stab him. Chuck managed to grab the blade before it stabbed him in the shoulder.

Chuck kicked him, causing the bad guy to fall backwards. As he fell, the blade moved across Chuck's hand, cutting it open. Chuck gasped in pain.

"That hurt," said Chuck, kicking the bad guy. He went down. However his colleague had recovered and came rushing towards Chuck.

"Seriously?" said Chuck. He managed to throw a couple of punches, but the man dodged them. He kicked Chuck causing him to fly backwards. He stumbled against the kitchen counter, using his hands to catch himself, not aware that he left a blood hand print.

Chuck launched forward, going into fight mode. The other guy was good. They continued to fight and Chuck became painfully aware of the mess they were making.

"Can you stop making a mess?" asked Chuck as he through another punch to the man's jaw. "My sister is going to kill me."

"Well we can't have that," Carl said from behind him. Chuck turned to face the new threat but he wasn't fast enough. Carl had Ellie's prized glass vase in his hand. He hit Chuck across the head with it, smashing it into a million pieces.

Chuck blinked and fell to the ground. His last conscious thought was _Ellie is going to kill me…._

* * *

><p>Insert evil laugh here.<p>

Please R&R! I love reviews!


	2. Chapter 2

Before the Storm

By RascalFlattsS

Disclaimer: Do not own Chuck

Some swearing and Chuck whumpage

I can't remember what is the name of the hospital is the Ellie and Devon work at. If anyone knows, please let me know!

* * *

><p><em>Westfield Hospital- Burbank, California<em>

Ellie could not focus. She felt distracted. She kept going over the fight with Chuck this morning.

"Everything okay baby?" asked Devon, wrapping his arms around her.

"Fine," mumbled Ellie.

Devon raised an eyebrow, "Honey, you're not that good of a liar. Now what's wrong?"

Ellie sighed. "I can't stop thinking about how I left things with Chuck this morning."

"Oh honey," said Devon. He bent down and gave her a kiss, "Chuck knows that you just want what's best for him."

"He could do so much more than work at the Buy More," said Ellie. "I don't understand why he insists on stay there-why he won't move on with his life and live up to his potential."

"Ellie," said Devon. He walked around and took her hands in his, "Chuck is an adult and he has to live his own life. And he has to make his own choices. So if he has a reason for staying at the Buy More, then I'm sure he has a good reason."

He gave her a kiss, "If it bugs you so much, run home quick and have a talk with Chuck."

"I think I will," said Ellie. She reached up and gave him a kiss. "Thanks baby.

* * *

><p><em>Barktowski-Woodcomb Residence-Burbank, California<em>

Ellie grabbed the door knob and was surprised when she found it locked. She knocked on the door, "Chuck? Are you home? Chuck!"

Ellie waited a few minutes before she started digging for her keys. She looked through the window, "C'mon Chuck," she yelled. "This isn't funny! Open the door!"

No response. She pulled out her house keys and stuck them in the lock.

"C'mon Chuck, don't be such a-"Ellie said as she opened the door. She looked around at the mess, "baby," she finished quietly.

"Chuck?" she called out cautiously. She moved forward slowly throughout the apartment. "Chuck, what happened?"

She walked forward, nervous. She walked into the kitchen. She heard the crunch of broken glass under her feet. She looked down and saw that her grandmother's vase was now in a thousand little pieces. But that wasn't what concerned her.

What concerned her were the little drops of blood littered among the glass.

She gasped and jumped back. Her eyes fell to the kitchen where she spotted the bloody handprint on her once white counter.

Ellie felt her heart stop as all of her worst nightmares were suddenly realized. "CHUCK!" Ellie screamed. She ran throughout the apartment, searching for her brother. "CHUCK WHERE ARE YOU? CHUCK!"

She searched every corner of the apartment, screaming for her brother to answer. After 5 minutes, she was forced to accept the horrible truth.

She collapsed on her bed and pulled out her cell phone.

Ellie waited until the 911 operated answer, "Someone broke into my house and kidnapped my little brother. You've got to find him! Please find him!

* * *

><p><em>Castle-Under the Burbank Buy More-Burbank, California<em>

"Where the hell is that moron?" growled Casey looking at his watch.

Sarah sighed, "Give him a break Casey. Between missions and the Buy More, he has been working non-stop. He deserves a little bit of a break."

Casey rolled his eyes and mumbled something under his breath.

The screen in front of them cracked and General Beckman came into view. "Colonel Casey, Agent Walker," she said. She looked around for Chuck. "And where is Agent Bartowski?"

Casey and Sarah shared a glance. "He's not—" Casey started.

"Here," finished Sarah quickly, "at the moment. But he should be on his way and arriving any moment."

General Beckman sighed, "I do not appreciate tardiness. I except all my agents to be on time to my-"General Beckman was cut off by the sound of an alarm going off in the background.

"What was that?" asked General Beckman but Casey and Sarah were already out of their seats and rushing over to the computers.

"Code 9," said Casey, as he read the computer. He paled, "Someone has made a 911 call from Bartowski apartment."

They looked at each other. If Chuck was in trouble, he would have activated the distress button on his watch to call Sarah and Casey. He wouldn't call 911.

But someone else would…someone who didn't know Chuck's secret….and if Chuck wasn't able to stop them from doing so….

"Play it," said Sarah. She tried to keep the fear out of her voice.

Casey nodded. He pressed the button. They heard Ellie's voice come over the line, crying. "_Someone broke into my house and kidnapped my little brother. You've got to find him! Please find him!_"

Sarah paled. She felt her legs turn to rubber. Her grip tightened on the desk. _If anything happens to him…_

She heard Casey talking to General Beckman in the background.

"Sorry General. We're going to have to call you back."

* * *

><p><em>Westfield Hospital-Burbank, California<em>

Devon was preparing to walk into surgery when his boss Dr. Shepard walked in, followed by his colleague Dr. Johnson.

"Devon," said Dr. Shepard. "Dave is going to cover the surgery for you today."

Dr. Shepard and Dr. Johnson both looked grim. Devon tried to smile.

"Everything is okay, I hope?" asked Devon.

Dr. Shepard sighed, "Ellie's fine."

Devon paled. "Of course Ellie's all right. Why wouldn't she be?"

"Devon," Dr. Johnson said. "Someone broke into your apartment. It appears they made a real mess of the place."

Devon relaxed, taking a deep breath. Then suddenly realization hit him like a freight train.

"Oh God," Devon whispered. "What about Chuck? Is he okay?"

The two men turned and looked at each other. Devon felt his stomach drop.

"Where's Chuck?" demanded Devon, afraid to hear the answer.

Dr. Shepard sighed, "Chuck's missing. The police believe he has been kidnapped."

* * *

><p><em>Secret Evil Guy Hiding Place-Location Unknown<em>

The first thing Chuck was aware of was the splitting headache. He had never had a headache this bad before. Not when the Intersect was first not uploaded, not when he had the upload, not when it was removed and then re-uploaded back into his head.

_This can only be a concussion….a really bad ass concussion…._

Chuck groaned and opened his eyes. The bright light blinded him, causing him to wince in pain.

"Aw, you're awake."

Chuck opened his eyes and saw Carl standing in front of him. Chuck looked up and saw that his wrists were tied up and suspended above his head. He was currently standing up right with his feet just barely touching the floor.

"You had to break my sister's favorite vase?" asked Chuck. "She is going to be super pissed."

"Oh I'm sure," said Carl. "Her 911 call was just heartbreaking."

Chuck paled. "What the hell did you do to her?" He growled.

Carl walked over and patted his face, "Oh relax Charles. I haven't done anything to your sister. Except this." He pulled out a tape recorder and pressed play.

Ellie's voice started to play, "_Someone broke into my house and kidnapped my little brother. You've got to find him! Please find him!"_

Carl hit the stop button. "She sounds very afraid, doesn't she?"

"Leave her alone!" shouted Chuck, struggling against his bonds.

"Relax Charles," said Carl. "I have no intention of hurting your beloved sister or her husband." He smiled. "I already have you."

"What do you want?" asked Chuck.

"I already told you," said Carl. "You, young Charles, are just bait."

"And what type of fish are you planning to catch?" asked Chuck. "Because if you wanted the marlin in Big Mike's office, all you had to do was ask."

Carl sighed. He snapped his fingers. One of his large goons came walking over. He had a baseball bat in his hand. Chuck cursed silent knowing exactly what was going to happen but he was powerless to stop it.

The goon swung the baseball bat connecting it with Chuck's ribcage. Chuck gasped in pain.

"Rudeness Charles," said Carl "is not appreciated."

"Duly noted," gasped Chuck.

"And to answer your other question," said Carl. He smiled, "I assume you have heard of Orion?"

Chuck paled. "No," he lied.

Carl snapped his fingers and the bat connected with his ribs. Chuck gritted his teeth.

"I don't appreciate lying either, Charles," said Carl. "Or do you prefer Chuck? I know your father calls you Charles." He smiled. "You are in this mess because of your father."

"What do you want with my father?" asked Chuck.

"My men have been searching for Orion for quite some time," said Carl. "But as I'm sure you are aware, Orion is a tough man to find. But he does have one weakness," he paused. "_You_."

"He won't come," said Chuck.

"Oh I think we both know he will," said Carl. "And you better pray he does, because otherwise, I am going to kill you."

"And you're not just going to kill me anyway?" asked Chuck.

"Maybe," said Carl. "Maybe not. But you are forgetting that I worked with your father," said Carl. "He used to talk about you all the time. You were his pride and joy."

"Here's what going to happen, Chuck," continued Carl. "Your sister has already discovered that you have been kidnapped and has contacted the police. Soon, she will call your father and inform him of your disappearance and he is going to come running to rescue his precious son."

"My team will find you," said Chuck.

Carl laughed. "Your team will never find _you_." He turned to his associate. "Make sure to make our new friend feel welcome." He paused. "But don't kill him. Orion won't come if he thinks his son is dead."

The man nodded and hit Chuck with the baseball bat. Chuck gasped in pain.

"What the hell was that for?" asked Chuck.

"Revenge," said Carl simply. "Your father should have never tried to double cross me."

"What are you talking about?" shouted Chuck.

"Why ruin the surprise?" asked Carl. "You'll find out soon enough." He closed the door with a snap.

Chuck bit his lip as the goon bit him a baseball, hitting him in his chest, shoulder and his legs. As he felt his right shoulder popped out of the joint, he felt a blinding wave of heat wash over him, submerging him into unconscious.

* * *

><p>Please R&amp;R!<p> 


	3. Chapter 3

Before the Storm

By RascalFlattsS

Disclaimer: Do not own Chuck.

Some itty bitty little spoilers for Season 3. And a little bit of AU from Chuck v. the Living Dead. But the story works a lot better is Stephen has a phone instead of using the codes through the classified.

* * *

><p><em>Somewhere in Southern California-Location Unknown<em>

Stephen J. Bartowski was sitting at his kitchen table when he heard a small ringing coming from his bookshelf. He walked up slowly moving toward the bookshelf. He slowly pulled out the book, revealing the cell phone that was currently ringing.

He pulled the phone out and answered it, "Hello?" he ask tentatively.

"_Dad," _gasped Ellie.

Stephen breathed a sigh of relief. However the relief was short lived once he heard the sadness in her voice, "Hi honey. Is everything okay?"

Ellie started crying, "_Dad, it's all my fault! We had a fight and now he's gone!"_

"Devon left?" asked Stephen surprised. He had a long talk with Devon before the wedding and Devon didn't seem like the leaving type.

"_No," _gasped Ellie, _"It's Chuck! They took him!" _

Stephen gasped. He grabbed the edge of the table with his hands, "What? What are you talking about Ellie? What happened?"

"_We had a fight," _said Ellie, _"I came back home to talk to him but he's not here! There's a mess-and oh my God, Dad, there's blood! Someone hurt Chuck! Why would someone hurt him, Dad?"_

Stephen took a deep breathing, trying to keep his fears at bay while he calmed his daughter, "Everything is going to be okay, Ellie. Your brother is strong and he's going to be fine." He rubbed his hand over his face. "Have you called the police?"

"_Yes," _said Ellie softly.

"Good," said Stephen. "And do they have any leads yet? Do they have any idea who would have taken him?"

"_No," _said Ellie, _"Who would want to hurt Chuck?" _She paused and Stephen was pretty sure she was wiping the tears off her face. _"Dad, I'm sorry." _

Stephen looked up confused, "For what?" he asked.

"_I was supposed to look out for him," _Ellie cried. _"I was supposed to protect him! And look what happened! It's all my fault!" _

_Oh honey, _thought Stephen, _it's my fault. I should have never left you or your brother alone…_

He took a deep breath, "It's not your fault, Ellie."

"_I can't lose him, Dad. If anything happens to him…"_

"Hey, listen to me," said Stephen firmly. "Everything is going to be fine. Your brother is strong and he is going to be just fine. I promise you that."

Stephen hung up the phone.

_When I find the SOB who hurt my son, they are going to pay. _

* * *

><p><em>In Route to the Bartowski-Woodcomb Residence-Burbank, California<em>

Devon had been through a lot of painstaking, hair-raising, adrenalin rushing events in his life. After all, he is rock-climbing, thrill seeking cardiologist.

But yet nothing has scared him like this.

Someone had broken into his apartment and had kidnapped Chuck. A million different thoughts ran through his mind. Who could be responsible for this? Fulcrum? The Ring? Who? Who would want to kidnap Chuck?

_A million different people, _thought Devon. Ever since he had learned for Chuck was a spy, he had become afraid for his safety and for Ellie's. He didn't really stop to think about Chuck's.

Until now.

Chuck had assured him that they had the best security system that money could buy. Casey had installed security cameras, microphones, bugs, transmitters and every other equipment a spy would ever need. Not to mention Casey lived right next door and Sarah practically lived at the apartment.

Nothing bad will ever happen to you or Ellie, Chuck had assured him, not while I'm around.

_But what about you Chuck? _Asked Devon, _who was there to protect you? _

Devon barely parked the car. He was out of the car before it even stopped. In two steps he was across the sidewalk and in the door. He ducked under the crime scene tape in one fluid motion.

The moment he walked through the door, he had a strong desire to run back out again.

The apartment looked like a tornado had hit it. Broken glass littered the floor. Items on the coffee table had been knocked over and the coffee table was lying on its side. Picture frames that had once lined the hall were now broken and on the floor. In their place were human size dents from figures being thrown against the wall.

Devon walked forward and saw Ellie's favorite vase broken in a thousand little pieces. In between the pieces were little drops of red.

Devon didn't have to guess what those were.

He looked up and saw the bloody handprint that now stood out on his kitchen counter. He suddenly felt sick.

"Buddy, you can't be here," said one of the cops, walking up to him, putting a hand on his shoulder. Devon starred at him in shock.

"It's okay," said Casey. He came walking up to Devon. "He's with me."

The cop nodded and walked off.

"You know him?" asked Devon still looking around at the scene before him.

Casey grunted. "I know lots of people."

"What happened?" asked Devon. He looked up at Casey.

Casey shrugged his shoulder. "Looks like a two-maybe three-man team." He sighed, "If it's any constellation, it looked like Bartowski put up one hell of a fight."

"It's not," said Devon bitterly, looking once again at his damaged apartment. He turned back to Casey. "Do you know who did this?"

Casey shook his head. "Not yet," he mumbled. "Did you notice any one hanging around? Anyone who looked out of place? Anything at all?"

Devon shook his head, "Nothing out of the ordinary," he answer. He looked around. "Where's my wife?"

Casey jerked his head. Devon followed. Among all the policemen and crime scene people, he saw Ellie sitting on the couch with Sarah.

Devon found himself moving through the crowd of people to get to his wife.

Five feet in front of the sofa, he stopped lost for words.

"Ellie-"

Ellie looked up. She got up and flung her arms around his neck, buried her head in his shoulder and started sobbing.

He immediately wrapped his arms around her. "It's going to be okay, baby. We're going to find him. I promise you baby, we're going to find him."

Over Ellie's shoulder, he saw John Casey nod in agreement.

* * *

><p><em>Secret Evil Guy Hiding Place-Location Unknown<em>

"You idiot! You were supposed to rough up a bit! Not dislocate his shoulder!"

Chuck gasped as sudden pressure was applied to his shoulder and there was a sicken pop and a flash of white hot pain as he shoulder was popped back into place.

"What difference does it make?"

"Because he works with computers, you idiot! He can't help his father on the Storm program if you hurt his hands!"

Chuck groaned as the pain lessened. After what felt like a million years, he opened his eyes.

He was no longer tied to ceiling but was rather lying on the floor. His hands were currently untied. He looked over at his right shoulder. It felt like it had been stepped on by an elephant. He wiggled his fingers. They moved. It hurt like hell but everything still worked.

"Aw, young Charles," said Carl, looking down at his guest. "You're awake, I see." He snapped his fingers and two guards came running over. They grabbed him and pulled him up off the floor. Chuck gasped as the one guard gripped his right arm.

"Easy now," said Carl. "I apologize for Liam. He was not supposed to dislocate your shoulder. However Adam here," he gestured to the guard on his left, "has managed to get your shoulder back into the socket without much difficultly."

"Thanks," mumbled Chuck.

Carl smiled. "Are you ready for the next stage in our plan?" he asked.

"Depends," said Chuck. "What is it?"

"Your sister has called your father to inform him of the situation," said Carl. "He is on his way but needs a little bit of direction finding our location. You-young Charles-are going to tell your father to come right away."

"There is no way in hell," growled Chuck, "That I am going to help you capture my father. And if you think anything otherwise, you must be out of your damn mind!"

Carl sighed. He punched Chuck in the ribs, hitting any already bruised rib. Chuck gasped in pain. He felt Carl grab his hair and pulled. Chuck gasped in pain as his head was lifted upwards and a gun was jammed under his chin.

"I admire your loyalty," said Carl. "But I can assure you Mr. Bartowski that I am not a man you want to as an enemy. Do you understand?"

"Yes," said Chuck softly.

Carl lowered the gun and released his grip on Chuck. Chuck let his head sank forward to his chest, breathing deeply.

"Time for phase two."

* * *

><p><em>Some Road in Southern California-Exact Location Unknown <em>

As soon as Stephen hung up the phone, he went to his bedroom and grabbed the duffel bag out from under his bed. He then grabbing the cell phone from the table and ran out the door from his jeep.

As soon as he buckled his seatbelt, he slammed his foot on the gas.

Every 30 seconds he looked at the cell phone sitting in the glove department. He was well aware that whoever had kidnapped Chuck would be definitely be tracing his cell phone. He had removed the GPS chip so there was no way they would be able to determine his location. But he was more than certain that they would call him on this phone to contact him for further instructions.

Stephen was certain that whoever had kidnapped Chuck had done so to get to him. There was no doubt that who had been sent to kidnap his son was a professional team. The fact that Ellie had said that they had left a mess clearly meant that they wanted their presence to be known scared him. Sarah and Casey would know right away if Chuck was missing….the fact that they made their presence known meant that they wanted Ellie to know …which meant they wanted _him _to know…

This meant they took Chuck as a way to get to him….

Stephen punched the wheel. How could he have let this happen? He should have done a better job of protecting his family…and now because of him his son was in danger.

_I don't care what it takes, _thought Stephen, _I'll do whatever it take to keep my son safe._

Stephen looked at the phone. "Ring damn it!" he yelled at it

On cue, the phone started to ring.

Stephen practically leapt across the seat to grab the phone, causing the car to veer into the other lane, scaring the daylights out of the other driver.

"Hello?" asked Stephen.

"_Hello Stephen. It's been a long time." _

Stephen mentally cursed. This was worse than he thought. "Carl," he growled. "Where the hell is my son?"

"_He's right here," _said Carl.

"Let me talk to him," demanded Stephan.

"_Why not?" _said Carl. _"Charles! You have a phone call!"_

There was a pause. _"Dad?"_

Stephen tightened his grip on the phone. "Charles? Are you okay? Have they hurt you?"

"_I can't complain," _said Chuck. Stephen sighed. He could tell by his son's voice that he had been hurt. He could feel his anger boiling.

"_Have you talked to Ellie?" _asked Chuck.

"Yeah, I did," said Stephen.

"_She must be really pissed about Grandma's vase," _said Chuck.

Stephen smiled slightly, "She's a few other things on her mind, kiddo."

"_Dad," _said Chuck, all the fun was gone from his voice, "_You can't come. They're not after me-they are after you. Please don't come for me. Please, Dad."_

"_SHUT UP!" _shouted Carl. Stephen heard the sound of someone getting hit and heard Chuck gasp in pain.

"If you hurt my son, I swear to God I will kill you," growled Stephen.

"_You should be proud," _ said Carl. _"Your son is a chip of the old block." _There was a pause, _"Now listen Stephen, if you want to ever see your son again, you need to do exactly what I say." _

* * *

><p>Another cliff hanger! Horrible, I know.<p>

3 chapters all in a row-I deserve a prize. Or a cookie. Yeah on second thought, I'd rather have the cookie... ;-)

Please leave happy reviews-they encourage me to update sooner.


	4. Chapter 4

Before the Storm

By RascalFlattsS

Disclaimer: I do not own Chuck.

Spoilers: Some little spoilers to Chuck vs. the Living Dead and Chuck vs. the Subway. And from Season 2 Chuck vs the Ring. Little teeny spoilers-so small that you will need a microscope to see them.

Some violence and mild swearing. And of course, Chuck whumpage!

Thank you all so much for your reviews! They make me so happy!

* * *

><p><em>Some Road in Southern California-Exact Location Unknown<em>

"I swear to God if you lay one hand on him," growled Stephen,

"_Please Stevie," _said Carl. _"We both know your threats are useless." _There was a pause. "_Relax Stevie, as long as you do what I say, your kid will be fine." _

"What do you want?" asked Stephen.

"_Well I said we'd come and get you," _said Carl, "_but we can't see to find you. Removed the GPS chip, did we?"_

"Might have," said Stephen. "How about I meet you somewhere?"

"_McCarthy Park," _said Carl. _"Be there in one hour. Or your kid dies."_

* * *

><p><em>Colonel John Casey's Apartment-Burbank, California <em>

"Something isn't right."

Sarah looked up at Casey. They were sitting in Casey's apartment, watching the surveillance footage from the Bartowski apartment.

_Of course, this isn't right, _thought Sarah, _Someone kidnapped Chuck! Someone hurt him…God only knows what is happening to him right now or if he is even still alive….._

"Earth to Walker! Hello?" asked Casey, waving his hand in front of her face.

"Oh I'm sorry Casey," said Sarah. "My mind was…elsewhere."

Casey grunted. "Watch this." He replayed the surveillance tape. "What do you see?"

Sarah sighed. "Chuck fighting with the kidnappers." She continued watching and then suddenly she grabbed the remote hitting the pause button.

"That's a standard CIA move," said Sarah slowly. "You think the Ring is behind this?"

Casey shrugged, "Most likely. But that's not what is bugging me." He hit the play button. "Watch the time stamp."

Sarah watched the time stamp. "8:30 am. So?"

"So watch this next part," said Casey. He fast forward. "This is when Ellie comes home and finds Bartowski missing. Now look at this time stamp."

"Quarter to one," said Sarah.

"We know that Bartowski was kidnapped around eight thirty this morning," said Casey. "And that the people who kidnapped him are professional CIA-most likely working for the Ring."

"Right," said Sarah.

"And we know Ellie doesn't come home till almost one to find Bartowski," said Casey. "So that leaves almost a four hour window from when Bartowski disappears to once it is found."

"Casey, what is the point?" asked Sarah.

"The kidnappers have a four hour window to clean up the mess," said Casey. "So why the hell didn't they?"

Sarah paused. Casey had a point. Why would the kidnappers leave such an obvious mess? Why would leave such an obvious clue?

"We're missing something," said Sarah. "I mean, we would know right away that Chuck is missing, why stage the apartment?"

"Because it's not meant for us," said Casey, suddenly. He jumps out and races out of the apartment. Sarah follows in hot pursuit.

"Casey! What's going on?" she yells.

Casey ignores her and continues running. He runs into the Bartowski-Woodcomb apartment. Devon and Ellie are sitting on the couch talking quietly. They both look up when Casey rushes in with Sarah right on his heels.

"Ellie," said Casey out of breath. "Have you received a ransom note yet?"

"No," said Ellie slowly.

"John is everything okay?" asked Devon.

"Did you tell anyone?" asked Casey. "Did you call anyone?"

"No," said Ellie. "I just called 911 and the hospital and…" She paled. "Oh God," she whispered as realization hit. She held her head in her hands as fresh tears started to flow.

"Ellie, who did you call?" demanded Casey.

"Dad," said Ellie. She looked up at them, "I called my dad."

* * *

><p><em>Burbank Buy More-Burbank, California <em>

Morgan Grimes could tell that this was going to be a long time when he arrived to work at the Buy More. However he had no idea.

He was helping a customer when he saw Big Mike waiving him over to his office.

"Will you excuse me for a moment?" asked Morgan. He walked over to Big Mike's office. "Whatever happened, I can assure you that I am in no way responsible…."

"Sit down, Morgan," said Big Mike. There was sadness in his voice that Morgan had never heard before. There were two police officers standing in the office with him.

"Is everything okay?" asked Morgan, afraid to ask. Big Mike shook his head.

"Mr. Grimes," said one of the officers. "I'm Officer Keller and this is Officer Hansen."

"Okay," said Morgan slowly. "What can I help you with?"

"Do you know a Chuck Bartowski?" asked Officer Keller.

Morgan nodded, "Yes. He's my best friend." He swallowed. "Why are you asking this?

"Someone broke into his apartment this morning," said Officer Keller.

"Oh my God," said Morgan. "Is Chuck okay?"

The two officers exchange a small glance. "What is it?" asked Morgan.

"Mr. Grimes, it appears your friend Chuck Bartowski has been kidnapped…

* * *

><p><em>Secret Evil Guy Hiding Place-Location Unknown<em>

Stephen had arrived at the park on time. Upon arriving, he had spotted a black SUV in the parking lot. He had left his car and walked over to the SUV. The guards had checked for any bugs or GPS trackers. Once they had been assured there was none, they had opened the trunk and advised that would be his seat for the journey.

To Carl's credit, the truck at least had plenty of leg space.

After several hours of driving, the SUV came to a stop. Once Stephen was let out of the truck, he looked around at his surrounds. From what he could tell, they were in the middle of the desert, with no sign of civilization anywhere.

_Great, _thought Stephen _that will make escaping a little tricky. _

The two guards had escorted into a large warehouse. The two men lead Stephen down a long hallway. Stephen wondered these men had not handcuffed his hands or why they were not more guards escorting him.

Finally after walking the length of a football field, the guards arrived at a door. The guards opened the door and roughly pushed Stephen in causing him to stumbled.

"Geez," said Stephen. "Take it easy. Push me again and I'll make you regret it."

"No, you won't." The voice caused Stephen to turn. He gasped.

Carl stepped forward. He was using Chuck as a human shield. He then had a gun pointed at his son's head.

"That's always been your weakness Orion," said Carl. "You were always a family man."

Stephen glared, "What do you want Carl?"

"Straight to the point as always," said Carl. "I'm working on a little project—one of the ones we were working on back in the day—and it's got a few bugs in it. And you seem like a perfect man for the job."

Stephen sighed, "I'm not helping you build another Intersect."

Carl rolled his eyes, "What is it with you Bartowskis and the Intersect?" he asked. "Why the hell would _you _to help me build an Intersect? I could an Intersect in my sleep." He smiled, "Besides why build a new Intersect when I already have the newest version?" Chuck paled.

"What the hell are you talking about?" growled Stephen.

Carl smiled, "You don't know?" he asked.

"Shut up!" shouted Chuck. "Don't listen to him Dad! He's—"

"SHUT UP!" roared Carl. He pushed the barrel harder into Chuck's skull. Chuck stopped talking.

"Your son is the new Intersect," said Carl.

"You're lying," said Stephen. "Bryce Larkin is the new Intersect."

"Bryce Larkin is dead," said Carl. "Your son and Larkin were the only ones in the room before the Intersect 2.0 was destroyed. Larkin is dead. It doesn't take a genius to figure it out." He smiled. "And if that's not enough proof for you, he'd flashed when we first met. In fact, I'm sure we can find something for him to flash on." He smiled, "Oh Ivan! Come here."

One of the guards, Ivan stepped forward. Stephen spared Ivan a quick glance before turning back to his son. He watched in horror as he saw Chuck flash. He saw his son's eyes roll up his head and move back and forward as the pictures and information flashed before him.

As the flash ended, Chuck shook his head, as if trying to shake the images from his mind.

"See what I mean?" said Carl. "Charles Irving Bartowski is the Intersect 2.0 and the CIA's newest spy!"

"Dad," whispered Chuck. He looked up at his father, his eyes pleading. "Dad, I'm so sorry. I was going to tell you—"

"Enough," said Carl. "Not that I am not enjoying this wonderful father-son moment but this isn't Dr. Phil." He paused, "I mean I have places to go, evil plans to set into place and a world to take over."

"Fine," said Stephen. "What the hell do you want?"

"I'm rebuilding the Storm," said Carl.

Stephen paled. "Are you crazy?" he asked.

Carl struggled. "Maybe a little. But I want Storm. And you're the first person I thought of for the job."

"I'm flattered," said Stephen.

"Here's my offer," said Carl. "You help me rebuild the Storm-solving all the little problems we ran into years ago and you and your son will walk out of here. Alive."

"Let Charles go first," said Stephen.

"No," said Carl.

"You let my son go right now or I'll _never_ help you," growled Stephen

"Yes you will," said Carl. He smiled. "Don't insult my intelligence, Stephen. I heard what happened with Roark. He was a nice guy and let your kid go. Then your son goes running back to his CIA handlers and a whole Fulcrum base ends up getting blown up to bits in an air strike. No offense, Stephen but that's not how this story goes."

"Here's my counter offer," said Carl. "Your son stays here until you complete the Storm project. Then once the project you and your son can walk away scotch free."

"No," said Stephen. He crossed his arms. "You let him go now or you can forget it."

Carl shrugged. "Fine. Have it your way." He pushed Chuck forward. Chuck caught off guard by the sudden moment and combined with the concussion, Chuck fell forward. He automatically threw his hands out to brace his fall. He tried not to cry out as pain flared up through his injury shoulder but he couldn't help but suppress a groan.

Chuck started to sit up. Carl kicked him in the chest, hitting his injured ribs. Chuck heard something snap as Carl's steel toe boots collided with his ribs. Chuck fell back, gasping in pain, trying to breathe.

"No!" Stephen started to move forward towards his injured son but two men grabbed his arm and drag him back. Stephen struggled against them. "Leave him alone!"

Carl smiled, "Hit a nerve, didn't I?" He kicked Chuck again. Chuck gasped, struggling to catch his breath.

"Wait till I get a hold of you," gasped Chuck, struggling to sit up. He started to sit up when Carl pushed him down with his boot, pinning him down to the floor. Chuck struggled to push the boot off of his chest but stopped when a gun was pointed at his chest.

"There are two ways this goes down Stephen," said Carl. "Option one; your son stays here while you complete the Storm project or option two; your son dies here and now." He cocked the gun.

"NO!" screamed Stephen. "No! I'll do it! I'll do whatever you want! Just don't hurt him!"

Carl smiled. "Now, see that wasn't so hard, was it?" he said. He lifted his boot off of Chuck. Chuck rolled over to his side, gasping and coughing.

"I have a few requests of my own," said Stephen.

Carl nodded, "Fine. Let's hear it."

"First, I want my son to stay with me," said Stephen.

"Of course," said Carl.

"Second, I want my son to receive medical treatment," said Stephen.

"I can't get you a doctor," said Carl. "Unless you want me to invite your daughter or son-or-law to this little party."

"Not necessary," said Stephen quickly. "I can treat Charles as long as I have all the supplies. Bandages, gauze, saline solution, iodine, antibiotics—"

"I get the drift," said Carl. "All right, Stevie Old Boy, you got a deal. But be warned, if you try to double cross me or cheat me, you will be sorry." He growled. Stephen nodded in understanding.

"All right, boys," said Carl. "Let him go." The two men released him and in an instant, he was by his son's side in an instant.

"Charles?" he asked softly.

Chuck opened his eyes. "Dad-"he started. He struggled to sit up. Stephen helped him up and then pulled him close in a hug.

"Dad, I'm—"

"Shh," said Stephen, holding his son tightly. "Everything is going to be okay, Charles. Everything is going to be okay.

* * *

><p>Please R&amp;R! I love reviews!<p> 


	5. Chapter 5

Before the Storm

By RascalFlattsS

Disclaimer: Do not own Chuck

Sorry I haven't written in a while. Work has been pretty busy but things have finally slowed down, giving me time to write.

I don't think there are any spoilers, at least none that I can think of. But there may be some small ones buried in there.

Enjoy.

* * *

><p><em>Secret Evil Guy Hiding Place-Location Unknown<em>

"Aw, isn't this sweet?" said Carl. "A wonderful father-son moment—it's like it popped out of a Disney movie." He paused. "Okay, enough of this. Adam, Ivan, take our guests to their room. We'll talk later."

He walked out of the room, leaving the Bartowski men alone with the two henchmen.

Adam stepped forward, "If either one of you tries anything, I will shoot the other. Understand?" Both men nodded. "Good, now get up."

Stephen turned to his son, "Can you get up?" he asked.

Chuck scoffed. "Of course I can," he said. He stood up but he stood up a little quicker than he should of because his head started to spin. He took a step forward and he felt himself stumbling forward and would have fallen flat on his face, except Stephen managed to grab his arm and stop him from falling.

Chuck smiled weakly, "I might have a small concussion."

"Might?" said Stephen, raising an eyebrow. He lifted Chuck's arm over his shoulder, helping to carry his son.

"Dad, I'm fine," said Chuck, "I can walk by myself."

Stephen rolled his eyes, "Humor your old man, Charles."

Adam and Ivan lead the two Bartowski men down a long (emphasize on the word "long") hall. As their walk progressed, it became evident to Stephen that Chuck's concussion was worse than he original thought. As the walk progressed, Chuck became deadweight and Stephen was practically dragging Chuck down the hall.

After an eternity (actually, it may have been more like ten minutes but it certainly felt like an eternity), they arrived at a large steel door. Adam unlocked the door using the electric pin pad. The heavy door swung open slowly.

"Get in," said Ivan, gestured Stephen and Chuck into the room, with his gun. Stephen walked into the room, half carrying his son into the room.

"You will find everything you need," said Adam shortly. "The boss will be in shortly to go over the plans with you." Adam smiled, "On behalf of the Ring, enjoy your stay."

And with that, the door closed shut.

* * *

><p><em>Burbank Buy More-Burbank, California<em>

When he reflect back on what he can only call the worst day of his life, Morgan did not really remember much. He knew the police had asked him questions in Big Mike's office, asking if he had any enemies or anyone who would want to hurt him.

"Who would want to hurt Chuck?" asked Morgan. "Everybody _loves _Chuck." Big Mike nodded in agreement.

"Was there anyone Chuck didn't get along with?" asked Officer Hansen.

"Chuck got along with everybody," said Morgan. "He's a great guy. The only person he hated was Bryce Larkin."

"Who's that?" asked Officer Keller.

"Chuck's college roommate," said Morgan. "He got Chuck kicked out of Stanford and then sleep with his girlfriend."

Officer Keller made a note on his pad, "We'll look into this Larkin guy."

"Don't bother," said Morgan. "He died two years ago."

Officer Keller sighed, "Is there anyone else?" he asked.

Morgan shook his head. "No. Chuck's one of the nicest person I have every meet. I can't think of anyone who would want to hurt him."

Morgan looked up at the two officers, "You're going to find him, right?"

The two officers exchange glances. "We're going to do our best, son, " said Officer Hansen.

Morgan shook his head, "That's not good enough." He stood up, knocking over the chair he was sitting in. He walked past the two officers and walked out of Big Mike's office.

Big Mike walked after him, "GRIMES! Where are you going?"

Morgan ignored him and continued walking and walked out the sliding doors.

Big Mike sighed. He looked at Jeff and Lester. "Well?" he asked.

"We're on it!" said Lester as he and Jeff jumped out from behind the Nerd Herd help desk and ran out of the store after Morgan.

* * *

><p><em>Bartowski-Woodcomb Residence-Burbank, California<em>

Devon watched as Sarah sat on the couch, counseling Ellie as she broke into a fresh set of tears. He was about to go over himself, but he found himself turning and walking over to John Casey's apartment. He didn't even bother knocking as he walked over in.

"Try knocking next time," said Casey. He was bent over his computer system and didn't even bother to look up as Devon walked in.

"What the hell is going on here Casey?" asked Devon. "You know who kidnapped Chuck, don't you?"

Casey ignored him. Devon grabbed him and threw him against the wall. "Tell me!" he demanded.

Casey sighed. He pushed past Devon. "Do that again, and you'll be in the hospital-as a patient."

Devon sighed. He rubbed his hands over his face. "I'm sorry."

Casey nodded, "And to answer your question, no, I don't know who kidnapped Chuck. But I think I know why he was kidnapped."

"It has something to do with Chuck and Ellie's dad doesn't it?" asked Devon softly.

Casey sighed. "How much do you know about your father-in-law?" asked Casey.

"Not much," said Devon. "I know he used to work with computers and that he left Chuck and Ellie when they were teenagers. And that's he's extremely paranoid. And he's a little crazy."

"He's not crazy," said Casey. He rubbed a hand over his face, "What I am about to tell you is classified information. And if you repeat it to _anyone, _I will throw in you in jail for treason. Understand?" Devon nodded.

"Stephen Bartowski used to work as a computer engineer for the CIA," said Casey. "He worked on a number of projects, including the Intersect."

"He worked on the Intersect?" asked Devon. "As in the Intersect that is in Chuck's head?"

"He invented it," said Casey, "Everything-including the idea behind a human intersect—it was all his idea. He is known by the code name Orion. He's one of the most brilliant computer engineers in the world. And anyone who would want to build their own Intersect-or any other computer program like it- would need him. The only problem is Orion is an impossible man to find. Unless—"

"unless you kidnap his son," finished Devon. "You think that's why Chuck was kidnapped."

Casey shrugged. "It's the most likely explanation I can come up with. Chuck was kidnapped at 8:30 this morning…"

"WHAT?" asked Devon. He stumbled backwards. Chuck had been hurt and alone since this morning? The kidnappers had arrived right after he and Ellie left for work…..

"Anyway," continued Casey, looking a little annoyed. "From the surveillance video, this was a profession team and yet they don't clean up after themselves? They leave the obvious clues of a struggle—why? They _want _us to know they took Chuck? Why? It didn't make any sense…unless Bartowski isn't the target but rather he's the bait….

"And I doubt anyone in the Ring would want you or Ellie. Or God forbid, that idiot Morgan. But for Stephen…well it worked before."

"Wait, wait," said Devon. "Someone kidnapped Chuck before?"

Casey sighed. "Do you remember when Stephen disappeared right before your wedding?" Devon nodded. "He was kidnapped by Fulcrum. They wanted him to build a new Intersect. They managed to capture Chuck and Stephen together. They were going to take Stephen and kill Chuck until Stephen revealed that Chuck was his son and begged them to let Chuck go. He agreed that if they let Chuck go and he would help them build a new Intersect. And it worked. They let Chuck go and Sarah and I managed to rescue him. Then we managed to find their hideout…well…let's just say it did not end well for Fulcrum.

"While it worked at the time because it saved Chuck's life," continued Casey, "it let the Ring and everyone else know whose Orion's son is and that he would do anything to protect him…."

"Making Chuck the perfect bait to lure Stephen," finished Devon. "This is good news! This means that they won't hurt Chuck, right? Right?"

"It means they have a reason to keep Chuck alive at the moment," said Casey slowly. "Until they get what they want from Stephen. But the moment they do, they have no reason to keep Stephen or Chuck alive."

* * *

><p><em>Secret Evil Guy Hiding Place-Location Unknown<em>

As soon as the door closed behind them, Stephen dragged Chuck over to a chair sitting at a table. He then grabbed the first aid kit that Carl had left on the table for them.

He opened it up and found several different sizes of bandages, gauze, medical tape, alcohol wipes**, **iodine, aspirin,Neosporin, rubber gloves, an ice pack, Ace bandage wrap and a sling.

"Not bad," said Stephen. "Now, let's get you get cleaned up."

"I'm fine," said Chuck.

"Sure you are," said Stephen. He grabbed the ice pack; shook it, breaking the little crystal and the ice pack suddenly became cold. He wrapped a piece of gauze around it and hanged it to Chuck. "Here. Hold to this on your head. It will help with that goose egg you got."

Chuck took the ice pack in his left hand and held up to his head. "Yeah, that would be were Carl broke Ellie's favorite vase."

Stephen could feel his anger rising. Chuck could feel the anger rolling off his father. "Really, Dad, I'm okay."

"No you're not," said Stephen. "I can only assume that you have a few fracture ribs, if not broken." He looked at the shock on Chuck's face. "I saw Carl kick you and I saw that he was wearing steel toed boots. It doesn't take a genius to put two and two together."

Chuck sighed. He set the ice pack down. Stephen winced as he saw the blood on the gauze.

"Your head's still not bleeding is it?" he asked.

"What?" asked Chuck. He looked at the gauze. "Oh. No, I think that's from this." He held out his left palm which had a large cut across it.

Stephen grabbed his son's hand. The cut looked like it had reopened and was now bleeding freely. Stephen cursed. It looked deep. And a little swollen. Which means it could already been infected.

"I need to get this cleaned up," said Stephen. He grabbed an alcohol wipe and ripped it open and began to clean the cut. Chuck gritted his teeth as the alcohol stung.

There were a few minutes of silence as Stephen cleaned the cut.

"Dad, I'm sorry," said Chuck breaking the silence. "I should have told you about the Intersect—"

"Why did you do it?" asked Stephen. "I thought you wanted it out of your head and not even a full day passes before you download it again!"

"I know," said Chuck. "I just-I didn't know what else to do! Bryce was dead and they were breaking down the door. I couldn't let them get the Intersect but I couldn't just destroy it either; it was your greatest creation. And I thought of all the good it could do — all the people it could save-that I could save and help…" He paused. "I thought I could be someone special and I could do great things."

"You don't need the Intersect to be someone special Charles," said Stephen softly.

"Thanks Dad," said Chuck. He hung his head. "I'm sorry about this Dad. I didn't mean to disappoint you-I just wanted to make you and Ellie proud. I suppose you probably hate me now."

"Hey," said Stephen. He lifted Chuck's head so that he was looking straight into his son's eyes. "You could never do anything that would make me hate you. Or be disappointed. I am so proud of you. I may not agree with your choice but you're a grown man and you have to make your own choices. And if this is what you want, then okay."

"Okay?" asked Chuck uncertain.

"Okay," said Stephen. "If this is what you want to do, then okay, I will be supportive."

Chuck smiled. "Thanks Dad."

"I'm sorry to hear about Bryce," said Stephen. "He was a good agent and a good man."

Chuck looked at his father, "You knew Bryce?"

"Yes, I did," said Stephen. He saw the puzzled look on Chuck's face. "When I learned your college roommate was a CIA agent, I wanted to meet him and talk to him."

"How do you know my roommate was a CIA agent?" asked Chuck.

"I'm Orion," said Stephen. "I was one of the best computer programmers the CIA ever had. You don't think I wasn't able to keep tabs on my own children?"

"So you've been keeping tabs on Ellie and me all this time?" asked Chuck.

"Of course," said Stephen. He put some of the iodine on a piece of gauze and rubbed it on Chuck's hand. "I'll let that dry before I wrap your hand up in gauze."

Chuck nodded. "Hey Dad? Can I ask you a question?"

Stephen nodded.

"What's Storm?" asked Chuck.

Stephen paused. "It's complicated…"

"I'm guessing it's some kind of computer system," said Chuck.

"It is," said Stephen. He sighed. "It's a long story."

Chuck looked around, "We've been kidnapped and have been locked in a giant cell. I think we have time."

Stephen smiled. He gently ruffled Chuck's hair. "It starts back in the early 1990's when I was working on the Intersect project. The Intersect was still in its infancy. At the time, the goal was design a supercomputer to hold all the government data and could look for and find patterns.

"As I'm sure you already know, Carl was a member of my team. He was in charge of designing the firewall for the Intersect. The firewall program he designed was called Storm."

"So the Storm is the firewall for the Intersect," said Chuck, "So does that mean that the Storm program is in my head?"

Stephen shook his head. "No. The Storm was _**supposed**_ to be the firewall for the Intersect. It turns out that not what Carl designed the Storm to do. The Storm that Carl designed is nothing like a firewall. It was designed to act as firewall when instead it was stealing data from the program it was protecting. The Storm was designed to steal information from the Intersect.

"Carl designed the Storm and we added it to the Intersect. Everything seemed to work just fine. The Storm repelled every virus and other attack we could throw at it. It seemed like a success.

"Carl didn't know that I had a back-up copy of the Intersect data. The reason was so that if anything happened while I was working with the program and any of the data was destroyed, I had another system that I could pull from. It was a failsafe, which did not have a copy of the Storm on it. One day, when I was doing regular diagnostics, I noticed that there was a difference between the bite sizes. The Intersect with the Storm had _fewer_ data bites when it should have had _more._

"So I ran some comparison tests. I noticed that data that was missing from the Intersect was on my back up system. At first, I thought it was a mistake-computer error. So I added the missing data back in and wrote in a new program that should have prevented the problem from occurring again."

"It didn't work, did it?" asked Chuck.

"No," said Stephen. "When I check a week later to check to make sure that program was working, I saw that the data I replaced was missing again and my computer program that I had added had been re-written by someone. More importantly, _more_ data was missing. And when I compared the data bites from the week before, it showed _more. _And when I compared to see percentage, the Storm was taking more space than it should have. And it was taking up more space than it had the week before. And there were no new additions to the Storm program to cause the increase in data bites."

"So you think someone added more to the Storm program to cover up the fact that they were stealing information from the Intersect?" asked Chuck.

Stephen nodded. "I knew this time it couldn't be computer error; someone was stealing information from the Intersect and was filling it with junk to hide the size difference. The Storm had found my program and that someone had re-written it to allow the Storm to keep stealing the data."

"What did you do?" asked Chuck.

"I created a Trojan horse," said Stephen. "I created a new file of data to add to the Intersect. At first glance, it looked like heavy duty secrets, so I was sure that the Storm program would steal it. But imbedded in the data was a heavy duty computer virus that would destroy the Intersect and the Storm program. It would also destroy whatever computer system the thief was using to store the data. I also created the virus to attach itself to the Storm program so that it would destroy every system that the Storm was on."

"You destroyed the Intersect?" asked Chuck.

"You're forgetting that I had a backup copy," said Stephen. "Charles, you have to understand. The Storm was stealing heavy duty government secrets and if those secrets got out…." He paused, "I had to stop the program or else the Intersect would be nothing but white noise. The next day, I added the file."

"What happened?" asked Chuck.

"It worked," said Stephen. "The Storm stole the file and removed it from the Intersect within ten minutes after I added it." He smiled. "I created the virus to attach itself to the Storm program and every computer the Storm program touched would have a copy of the virus destroying the computer system. Which it did. It destroyed the Intersect and the Storm….and Carl's computer. It fried his system, destroying everything.

"At that point, I knew who the thief was. I couldn't believe it. Carl was my friend. He and his wife came over from brunch on Sunday; you played with his son, Jacob."

"I remember…" said Chuck softly. "What happened then?"

"What do you think?" said Stephen. "I turned him in. He went to jail for treason. Turns out he was selling the data to our enemies. I heard that his wife divorced him and she and Jacob moved out of California.

"After that I redesigned the Intersect and created my own firewall program-one that was designed to block and destroy computer programs like the Storm.. I hired a new team and the new Intersect was born."

"So the Storm program," said Chuck slowly. "It can steal data from the Intersect? In my head?"

"Oh no," said Stephen as he wrapped Chuck's hand in gauze. "Like I said, the Intersect has _my_ firewall program that protects the Intersect from programs like the Storm. Besides, your own brain acts like an additional firewall for the Intersect, protecting it from programs like the Storm. The Storm program can only get data from _computers_….that's why I worked so hard on the human intersect…because it was the one way to protect the Intersect from Carl and the Storm forever…."

"So what does Carl plan to use the Storm for?" asked Chuck. "He must know that after you caught him that you would redesign the Intersect to protect it from the Storm."

Stephen shook his head, "I don't know what he wants," he said. "Or what he's after. But if he's planning on bring back the Storm program, you know it can't be anything good."

* * *

><p>There you are…just a little itty bitty cliff hanger<p>

Please R&R! I love reviews! They make me happy!


	6. Chapter 6

Before the Storm

By RascalFlattsS

Disclaimer: Do not own Chuck.

Warnings: Some Charah involved. Nothing too bad, I promise.

Thank you for all your reviews and your patience! Life has been so busy but now it has slowed down finally! Which means more time for FanFiction! Yay!

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><p><em>Secret Evil Guy Hiding Place-Location Unknown<em>

Stephen Bartowski had never felt so helpless.

His son has been kidnapped and badly injured. Chuck has a concussion, a bad cut on his left hand, injured right shoulder and 2 broken ribs. Not to mention numerous other scratches and bruises.

Stephen watched as his son sleep. He had just woken Chuck up for a concussion check. When he advised Chuck why he was waking him up, Chuck just rolled his eyes.

"I've had concussions before, Dad," said Chuck. He then rolled over and went back to bed.

When had Chuck ever had a concussion? But then there was so much of Ellie's and Chuck's childhood that he had missed.

He never wanted to leave them. It had broken his heart and ripped out his soul the day he walked out on his children. But it was the only thing he could think of. A group of Ukrainians were closing in, searching for Orion and the Intersect. Stephen thought he could handle anything…until the day the black van showed up outside his house and tried to attack the house…with his children inside. Fortunately, Stephen managed to take care of them before they could get to his children. But he knew he had to leave them; it was the only way to keep them safe.

But yet despite everything Stephen did, the Intersect had found its way to Chuck. Despite all the precautions that he had taken-that Bryce had taken-Chuck had gotten the Intersect and become part of the CIA. The life Stephen had spent so much time and energy keeping his son away from had found him. And then despite all the work, he had done to remove the Intersect from Chuck's head, Chuck downloaded it again.

It wasn't that Stephen wasn't proud of his son because he was. He just wanted to keep his son safe.

And yet, here he was. Kidnapped and held hostage, being forced to rebuild the Storm project or else his son would die.

"Aw Mary," Stephen whispered softly. "What am I going to do?"

But there was only one thing to do. He would do whatever it takes to keep his son safe.

Whatever it takes.

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><p><em>Bartowski-Woodcomb Residence-Burbank, California<em>

Ellie Bartowski-Woodcomb had never felt so helpless.

Her brother had been kidnapped. He was probably hurt and scared out of his mind. God only knows where he was or what his kidnappers had done to him.

Chuck was her little brother. The little brother she had sworn to protect, no matter what. And now, he was just gone.

Ellie was so scared that she never see him again.

Then, to make matters worse, Ellie had called her father. She had hoped that her father would come and help her get through this. She needed her father to get her through this. Her goal had bring her other member of her family in, to make sure he was safe. Instead, she had lead her father into a trap that had gotten him kidnapped him as well.

Her whole family. Gone.

Sarah had told her that it wasn't her fault. "Your father loves you and Chuck," Sarah had said. "I could tell when I meet him. He would have done anything for Chuck. This isn't your fault."

But it was her fault. She had left the apartment, angry at her brother, saying words that she hadn't meant; words she could never take back.

"Ellie," said Devon, "Is there anything I can get you?"

Ellie dried her eyes, "No honey."

Devon sat down next to her and took her hand, "He's going to be okay."

"You don't know that," said Ellie.

"I know Chuck," said Devon. "He's smart. He's tougher than he looks. He'll be fine."

"I can't lose him, Devon," said Ellie.

"Everyone is doing everything they can to find Chuck and your dad," said Devon. "Everything's going to be okay."

Everything was far from okay. And nothing was going to be okay for Ellie Bartowski-Woodcomb until her brother and father were safe and back home with her.

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><p><em>Bartowski-Woodcomb Residence-Burbank, California<em>

Devon Woodcomb had never felt so helpless.

His brother-in-law was missing. His father-in-law was missing. His beautiful strong wife was in their room, crying and nothing Devon did could make it better.

Devon had sat with Ellie until she fell into a restless sleep. Devon then slipped out from under her small form, gently laid her in bed and pulled the covers over in her.

He then marched over into Casey's apartment. He didn't even bother knocking just walked in. "Anything?" he asked.

Casey looked up and shook his head. "Nothing yet."

"What do you mean 'nothing?'" shouted Devon.

"We are doing everything we can to find him," said Casey. "Every agency, every person, every resource we have is looking for Bartowski right now. We will find him."

"Before or after they kill him?" asked Devon sarcastically.

"Devon," said Sarah softly. "We're going to find him, I promise. We have everyone working on this."

"Not everyone," said Devon. He looked up, "Let me help."

Casey and Sarah shared a look, "Devon, I don't think that's a good idea," said Sarah.

"Why not?" said Devon. "I can help!"

"You're too close to this," said Casey.

"Of course, I'm close to this!" shouted Devon. "That's my brother-in-law out there! Hell, I'm closer to Chuck than I am to my own brothers! God only knows where he is or what's happening to him! You can't possible understand-"

Devon paused, taking a deep breath, "I can't stand sitting around the house; just waiting. I need to help find him." He looked at them. "Please."

Casey nodded, "Alright, you can help. But you do what we say, when we said it. Understand?"

Devon nodded. "Thank you."

"Don't make me regret this Woodcomb," growled Casey. He pointed to a computer screen, "You can review the reports-let us know if anything pops."

Devon nodded and walked over to the computer, happy to being doing something. He hoped now that he was an active part of the investigation; the guilt that he was feeling might go away.

It didn't.

Devon sighed rubbing a hand over his face. "C'mon Chuck. Help me find something to find you."

Because this was definitely _not_ awesome.

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><p><em>Colonel John Casey's Residence-Burbank, California<em>

Colonel John Casey had never felt so helpless in his life.

Casey wasn't really sure when it happened. This was supposed to be a baby-sitting. Wait Bartowski. Keep him and the Intersect safe. Simple. Easy. Then it turned into take the Intersect out on missions. Keep Bartowski from get killed or kidnapped, ect.

But the important number one John Casey rule was to keep your distance.

He had to admit that Walker was a damn good partner-the best he had. He had been skeptical about her at first but she had been able to pull her own-and then some.

And then there was Bartowski. Casey had watched as Chuck developed into an agent and watch him grow into the man he has become; more sure, more confident. While Casey wished that Chuck had more combat training and was more like the soldiers he was used to working with, he couldn't help but admire Chuck's loyalty for his friends and family. No matter what the risk to himself or the mission, Bartowski would never leave a man (or woman) behind.

Between the three of them, they made an unstoppable team. There was no mission they couldn't handle. Chuck, Ellie and Devon had invited them into their home and before he knew it, Casey didn't just have a team; he had a family.

It had taken him ten years to find a family again; he wasn't going to let anyone take it away from him. No matter what it takes, Casey was going to get his family back.

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><p><em>Colonel John Casey's Residence-Burbank, California<em>

Sarah Walker had never felt so hopeless.

Chuck was her asset. She was supposed to protect him. She was supposed to keep him safe. He was her responsibility.

And she had let him down.

Sarah sighed, rubbing her hand over her hand. How could this happened? How could they have let someone get to Chuck?

The bad guys had removed Chuck's watch. And they had found his cell phone on the floor in Ellie's room. There was no way to trace Chuck and find him; not until they found out who had taken him.

When they found that Ellie had called Orion, they were hopefully that he would lead them to Chuck but so far nothing. There was no chatter or noise or _anything. _It was like Chuck had fallen off the face of the earth.

Sarah took a deep breath. She needed to be calmed. She needed to focus. Chuck _needed _her to focus. She had to keep her emotions at bay.

But at this moment, she was finding it harder than ever.

_When are you going to admit it? _She thought. She tried so hard to hide her feelings but Chuck. She tried to tell herself that it wasn't real, it was just a mission. But even she had a hard time believing that.

Sarah smiled. She loved everything about Chuck. He was sweet and kind, loyal, and smart. He was so smart; Sarah was always impressed with what Chuck could do with a computer. He was funny; he always find a way to make her smile. And he was great on missions. Not everyone could handle the responsibility of the Intersect but Chuck had risen to the occasion, surprising everyone. And dispute everything Chuck had been through, he still had a child-like innocent and the ability to trust that made her love him even more.

_Who am I kidding? _Though Sarah. She was head over heels in love with Chuck.

Sarah was going to find him and bring him home. And that as soon as he was safe in her arms, she was going to tell him exactly how she feels.

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><p><em>Secret Evil Guy Hiding Place-Location Unknown<em>

Chuck Bartowski had never felt so helpless.

He had been beat up, captured and was only God knows where he was. He had no way of contact his team for a rescue and his father had been captured right along with him.

So much for Chuck Bartowski: the world's greatest spy.

Chuck sighed. He tried closing his eyes but the marching band that just moved into his head wouldn't let him rest. The Intersect and concussions don't mix because when the pain would flare up, the Intersect would flash as if a flash would cure the pain. All it did was multiply it.

Chick sat up, rubbing his head as another flash came on (something about polka dancing). He heard his dad sleeping on the bunk above him. He was almost tempted to wake up his dad to ask him about the Intersect but he decided against it.

His dad had enough problems right now.

He really wished the Intersect would flash on something useful; that would get him and his dad out this mess. Somehow, he didn't see how polka dancing as useful in this mission.

Chuck wished for the thousand time that the Intersect had something about the Storm program in it. But alas-his dad had done an excellent job removing any reference to the Storm project from the Intersect.

Looks like this one is all on Chuck Bartowski.

Luckily for Chuck, computers and computer related things are his specialty.

Chuck doubted that he could rewrite the program in Storm to fundamentally change the program without his father or Carl knowing. But if only there was a way….to divert the Storm program without changing the program…without anyone noticing…

Suddenly, Chuck had an idea. An idea that would stop the Storm project in its tracks. The Storm project that was going to be Carl's saving grace was going to become his double edge sword.

And Charles Bartowski was just the spy for the job.

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><p>Please R&amp;R!<p> 


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